Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 213:2a4e1f7de5ab
remove calls to deprecated classes of JsonCpp
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 22 Dec 2020 09:28:30 +0100 |
parents | a1c265cb2174 |
children | 1e864138f0da |
rev | line source |
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0 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
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5 * Copyright (C) 2017-2020 Osimis S.A., Belgium |
0 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU Affero General Public License | |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
19 **/ | |
20 | |
21 | |
22 #include "../Framework/Algorithms/ReconstructPyramidCommand.h" | |
23 #include "../Framework/Algorithms/TranscodeTileCommand.h" | |
24 #include "../Framework/DicomToolbox.h" | |
25 #include "../Framework/DicomizerParameters.h" | |
26 #include "../Framework/ImagedVolumeParameters.h" | |
27 #include "../Framework/Inputs/HierarchicalTiff.h" | |
28 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
29 #include "../Framework/Inputs/TiledJpegImage.h" | |
30 #include "../Framework/Inputs/TiledPngImage.h" | |
31 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
151 | 32 #include "../Framework/MultiThreading/BagOfTasksProcessor.h" |
0 | 33 #include "../Framework/Outputs/DicomPyramidWriter.h" |
34 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
35 | |
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36 #include <Compatibility.h> // For std::unique_ptr |
192 | 37 #include <DicomParsing/FromDcmtkBridge.h> |
38 #include <Logging.h> | |
39 #include <OrthancException.h> | |
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40 #include <Toolbox.h> |
192 | 41 #include <SystemToolbox.h> |
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42 |
0 | 43 #include "ApplicationToolbox.h" |
44 | |
45 #include <EmbeddedResources.h> | |
46 | |
47 #include <dcmtk/dcmdata/dcdeftag.h> | |
48 #include <dcmtk/dcmdata/dcuid.h> | |
49 #include <dcmtk/dcmdata/dcvrobow.h> | |
50 #include <dcmtk/dcmdata/dcvrat.h> | |
51 | |
52 | |
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53 static const char* OPTION_COLOR = "color"; |
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54 static const char* OPTION_COMPRESSION = "compression"; |
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55 static const char* OPTION_DATASET = "dataset"; |
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56 static const char* OPTION_FOLDER = "folder"; |
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57 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
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58 static const char* OPTION_HELP = "help"; |
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59 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
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60 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
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61 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
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62 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
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63 static const char* OPTION_INPUT = "input"; |
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64 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
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65 static const char* OPTION_LEVELS = "levels"; |
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66 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
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67 static const char* OPTION_MAX_SIZE = "max-size"; |
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68 static const char* OPTION_OFFSET_X = "offset-x"; |
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69 static const char* OPTION_OFFSET_Y = "offset-y"; |
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70 static const char* OPTION_OPENSLIDE = "openslide"; |
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71 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
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72 static const char* OPTION_PYRAMID = "pyramid"; |
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73 static const char* OPTION_REENCODE = "reencode"; |
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74 static const char* OPTION_REPAINT = "repaint"; |
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75 static const char* OPTION_SAFETY = "safety"; |
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76 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
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77 static const char* OPTION_SMOOTH = "smooth"; |
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78 static const char* OPTION_THREADS = "threads"; |
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79 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
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80 static const char* OPTION_TILE_WIDTH = "tile-width"; |
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81 static const char* OPTION_VERBOSE = "verbose"; |
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82 static const char* OPTION_VERSION = "version"; |
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83 |
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84 |
0 | 85 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
86 OrthancWSI::ITiledPyramid& source, | |
87 const OrthancWSI::DicomizerParameters& parameters) | |
88 { | |
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89 LOG(WARNING) << "Transcoding the source pyramid (not re-encoding)"; |
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90 |
0 | 91 Orthanc::BagOfTasks tasks; |
92 | |
93 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
94 { | |
95 LOG(WARNING) << "Creating level " << i << " of size " | |
96 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
97 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
98 } | |
99 | |
100 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
101 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
102 } | |
103 | |
104 | |
105 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
106 OrthancWSI::ITiledPyramid& source, | |
107 const OrthancWSI::DicomizerParameters& parameters) | |
108 { | |
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109 LOG(WARNING) << "Re-encoding the source pyramid (not transcoding, slower process)"; |
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110 |
0 | 111 Orthanc::BagOfTasks tasks; |
112 | |
113 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
114 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
115 assert(levelsCount >= 1); | |
116 | |
117 for (unsigned int i = 0; i < levelsCount; i++) | |
118 { | |
119 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
120 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
121 | |
122 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
123 target.AddLevel(width, height); | |
124 } | |
125 | |
126 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
127 if (lowerLevelsCount > levelsCount) | |
128 { | |
129 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
130 << ") exceeds the number of levels (" << levelsCount | |
131 << "), cropping it"; | |
132 lowerLevelsCount = levelsCount; | |
133 } | |
134 | |
135 assert(lowerLevelsCount <= levelsCount); | |
136 if (lowerLevelsCount != levelsCount) | |
137 { | |
138 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
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139 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
0 | 140 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
141 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
142 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
143 | |
144 assert(tasks.GetSize() == 0); | |
145 | |
146 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
147 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
148 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
149 (tasks, target, truncated.GetUpperLevel(), | |
150 upperLevelsCount, lowerLevelsCount, parameters); | |
151 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
152 } | |
153 else | |
154 { | |
155 LOG(WARNING) << "Constructing the pyramid"; | |
156 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
157 (tasks, target, source, levelsCount, 0, parameters); | |
158 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
159 } | |
160 } | |
161 | |
162 | |
163 static void Recompress(OrthancWSI::IFileTarget& output, | |
164 OrthancWSI::ITiledPyramid& source, | |
165 const DcmDataset& dataset, | |
166 const OrthancWSI::DicomizerParameters& parameters, | |
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167 const OrthancWSI::ImagedVolumeParameters& volume, |
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168 OrthancWSI::ImageCompression sourceCompression) |
0 | 169 { |
170 OrthancWSI::TiledPyramidStatistics stats(source); | |
171 | |
172 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth() << "x" << stats.GetTileHeight(); | |
167
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173 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
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174 LOG(WARNING) << "Source photometric interpretation: " << Orthanc::EnumerationToString(source.GetPhotometricInterpretation()); |
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175 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
0 | 176 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
177 | |
178 if (parameters.IsRepaintBackground()) | |
179 { | |
180 LOG(WARNING) << "Repainting the background with color: (" | |
181 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
182 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
183 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
184 } | |
185 else | |
186 { | |
187 LOG(WARNING) << "No repainting of the background"; | |
188 } | |
189 | |
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190 Orthanc::PhotometricInterpretation targetPhotometric; |
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191 bool transcoding; |
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192 |
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193 if (parameters.IsForceReencode() || |
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194 parameters.IsReconstructPyramid() || |
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195 sourceCompression != parameters.GetTargetCompression()) |
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196 { |
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197 // The tiles of the source image will be re-encoded |
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198 transcoding = false; |
171 | 199 |
200 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
201 { | |
202 targetPhotometric = source.GetPhotometricInterpretation(); | |
203 } | |
204 else | |
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205 { |
171 | 206 switch (parameters.GetTargetCompression()) |
207 { | |
208 case OrthancWSI::ImageCompression_Jpeg: | |
209 case OrthancWSI::ImageCompression_Jpeg2000: | |
210 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
211 break; | |
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212 |
171 | 213 case OrthancWSI::ImageCompression_None: |
214 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
215 break; | |
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216 |
171 | 217 default: |
218 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
219 } | |
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220 } |
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221 } |
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222 else |
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223 { |
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224 // Transcoding: The tiles are copied (no re-encoding) |
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225 transcoding = true; |
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226 targetPhotometric = source.GetPhotometricInterpretation(); |
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227 } |
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228 |
0 | 229 OrthancWSI::DicomPyramidWriter target(output, dataset, |
230 source.GetPixelFormat(), | |
231 parameters.GetTargetCompression(), | |
232 parameters.GetTargetTileWidth(source), | |
233 parameters.GetTargetTileHeight(source), | |
234 parameters.GetDicomMaxFileSize(), | |
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235 volume, targetPhotometric); |
29 | 236 target.SetJpegQuality(parameters.GetJpegQuality()); |
0 | 237 |
238 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
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239 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
0 | 240 |
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241 if (!transcoding && |
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242 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
0 | 243 { |
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244 LOG(WARNING) << "Target compression: Jpeg with quality " |
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245 << static_cast<int>(target.GetJpegQuality()); |
0 | 246 target.SetJpegQuality(target.GetJpegQuality()); |
247 } | |
248 else | |
249 { | |
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250 LOG(WARNING) << "Target compression: " |
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251 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
0 | 252 } |
253 | |
254 if (stats.GetTileWidth() % target.GetTileWidth() != 0 || | |
255 stats.GetTileHeight() % target.GetTileHeight() != 0) | |
256 { | |
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257 LOG(ERROR) << "When resampling the tile size, " |
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258 << "it must be a integer divisor of the original tile size"; |
0 | 259 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
260 } | |
261 | |
262 if (target.GetTileWidth() <= 16 || | |
263 target.GetTileHeight() <= 16) | |
264 { | |
265 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
266 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
267 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
268 } | |
269 | |
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270 if (transcoding) |
0 | 271 { |
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272 TranscodePyramid(target, stats, parameters); |
0 | 273 } |
274 else | |
275 { | |
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276 ReconstructPyramid(target, stats, parameters); |
0 | 277 } |
278 | |
279 target.Flush(); | |
280 } | |
281 | |
282 | |
283 | |
284 static DcmDataset* ParseDataset(const std::string& path) | |
285 { | |
286 Json::Value json; | |
287 | |
288 if (path.empty()) | |
289 { | |
290 json = Json::objectValue; // Empty dataset => TODO EMBED | |
291 } | |
292 else | |
293 { | |
294 std::string content; | |
43 | 295 Orthanc::SystemToolbox::ReadFile(content, path); |
0 | 296 |
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297 if (!Orthanc::Toolbox::ReadJsonWithoutComments(json, content)) |
0 | 298 { |
299 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
300 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
301 } | |
302 } | |
303 | |
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304 std::unique_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1, |
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305 "" /* no private tag, thus no private creator */)); |
0 | 306 if (dataset.get() == NULL) |
307 { | |
308 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
309 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
310 } | |
311 | |
312 // VL Whole Slide Microscopy Image IOD | |
313 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.77.1.6"); | |
314 | |
315 // Slide Microscopy | |
316 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
317 | |
318 // Patient orientation makes no sense in whole-slide images | |
319 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
320 | |
321 // Some basic coordinate information | |
322 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
323 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
324 | |
325 std::string date, time; | |
130 | 326 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
0 | 327 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
328 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
329 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
330 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
331 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
332 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
333 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
334 | |
335 return dataset.release(); | |
336 } | |
337 | |
338 | |
339 | |
340 static void SetupDimension(DcmDataset& dataset, | |
341 const std::string& opticalPathId, | |
342 const OrthancWSI::ITiledPyramid& source, | |
343 const OrthancWSI::ImagedVolumeParameters& volume) | |
344 { | |
83 | 345 // Extract the identifier of the Dimension Organization, if provided |
346 std::string organization; | |
0 | 347 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
348 | |
83 | 349 if (previous != NULL && |
350 previous->tagExists(DCM_DimensionOrganizationUID)) | |
351 { | |
352 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
353 } | |
354 else | |
0 | 355 { |
83 | 356 // No Dimension Organization provided: Generate an unique identifier |
357 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
358 } | |
359 | |
360 | |
361 { | |
362 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
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363 std::unique_ptr<DcmItem> item(new DcmItem); |
83 | 364 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
365 | |
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366 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); |
83 | 367 |
368 if (!sequence->insert(item.release(), false, false).good() || | |
369 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
0 | 370 { |
83 | 371 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
0 | 372 } |
373 } | |
374 | |
83 | 375 |
0 | 376 { |
83 | 377 // Construct tag "Dimension Index Sequence" (0020,9222) |
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378 std::unique_ptr<DcmItem> item(new DcmItem); |
83 | 379 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
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380 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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381 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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382 |
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383 std::unique_ptr<DcmItem> item2(new DcmItem); |
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384 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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385 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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386 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
0 | 387 |
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388 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
0 | 389 |
83 | 390 if (!sequence->insert(item.release(), false, false).good() || |
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391 !sequence->insert(item2.release(), false, false).good() || |
83 | 392 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
393 { | |
394 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
395 } | |
0 | 396 } |
397 | |
398 | |
83 | 399 { |
400 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
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401 std::unique_ptr<DcmItem> item(new DcmItem); |
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402 |
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403 std::unique_ptr<DcmItem> item3(new DcmItem); |
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404 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
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405 |
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406 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
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407 std::unique_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
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408 |
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409 if (!sequence3->insert(item3.release(), false, false).good() || |
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410 !item->insert(sequence3.release(), false, false).good() || |
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411 !sequence->insert(item.release(), false, false).good() || |
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412 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
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413 { |
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414 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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415 } |
0 | 416 } |
417 } | |
418 | |
419 | |
420 static void EnrichDataset(DcmDataset& dataset, | |
421 const OrthancWSI::ITiledPyramid& source, | |
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422 OrthancWSI::ImageCompression sourceCompression, |
0 | 423 const OrthancWSI::DicomizerParameters& parameters, |
424 const OrthancWSI::ImagedVolumeParameters& volume) | |
425 { | |
426 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
427 | |
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428 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
0 | 429 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
430 { | |
431 // Takes as estimation a 1:10 compression ratio | |
432 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
433 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
434 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
435 } | |
436 else | |
437 { | |
438 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
439 } | |
440 | |
441 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
442 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
443 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
444 | |
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445 std::unique_ptr<DcmItem> origin(new DcmItem); |
0 | 446 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, |
447 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
448 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
449 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
450 | |
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451 std::unique_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); |
0 | 452 if (!sequenceOrigin->insert(origin.release(), false, false).good() || |
453 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
454 { | |
455 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
456 } | |
457 | |
458 | |
459 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
460 { | |
461 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
462 { | |
463 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
464 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
465 } | |
466 | |
467 std::string brightfield; | |
468 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
469 | |
470 Json::Value json; | |
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471 if (!Orthanc::Toolbox::ReadJsonWithoutComments(json, brightfield)) |
0 | 472 { |
473 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
474 } | |
475 | |
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476 std::unique_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( |
0 | 477 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), |
478 DCM_OpticalPathSequence.getElement()), | |
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479 json, false, encoding, |
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480 "" /* no private tag, thus no private creator */)); |
0 | 481 if (!dataset.insert(element.release()).good()) |
482 { | |
483 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
484 } | |
485 } | |
486 | |
487 | |
488 std::string profile; | |
489 if (parameters.GetIccProfilePath().empty()) | |
490 { | |
491 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
492 } | |
493 else | |
494 { | |
43 | 495 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
0 | 496 } |
497 | |
498 | |
499 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
500 if (opticalPath == NULL) | |
501 { | |
502 LOG(ERROR) << "No optical path specified"; | |
503 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
504 } | |
505 | |
506 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
507 { | |
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508 std::unique_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); |
0 | 509 |
510 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
511 !opticalPath->insert(icc.release()).good()) | |
512 { | |
513 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
514 } | |
515 } | |
516 | |
517 const char* opticalPathId = NULL; | |
518 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
519 opticalPathId == NULL) | |
520 { | |
521 LOG(ERROR) << "No identifier in the optical path"; | |
522 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
523 } | |
524 | |
525 SetupDimension(dataset, opticalPathId, source, volume); | |
526 } | |
527 | |
528 | |
529 static bool ParseParameters(int& exitStatus, | |
530 OrthancWSI::DicomizerParameters& parameters, | |
531 OrthancWSI::ImagedVolumeParameters& volume, | |
532 int argc, | |
533 char* argv[]) | |
534 { | |
535 // Declare the supported parameters | |
536 boost::program_options::options_description generic("Generic options"); | |
537 generic.add_options() | |
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538 (OPTION_HELP, "Display this help and exit") |
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539 (OPTION_VERSION, "Output version information and exit") |
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540 (OPTION_VERBOSE, "Be verbose in logs") |
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541 (OPTION_THREADS, |
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542 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
0 | 543 "Number of processing threads to be used") |
129
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544 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
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545 "Path to the shared library of OpenSlide " |
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546 "(not necessary if converting from standard hierarchical TIFF)") |
0 | 547 ; |
548 | |
549 boost::program_options::options_description source("Options for the source image"); | |
550 source.add_options() | |
129
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551 (OPTION_DATASET, boost::program_options::value<std::string>(), |
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552 "Path to a JSON file containing the DICOM dataset") |
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553 (OPTION_SAMPLE_DATASET, |
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554 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
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555 (OPTION_REENCODE, boost::program_options::value<bool>(), |
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556 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
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557 (OPTION_REPAINT, boost::program_options::value<bool>(), |
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558 "Whether to repaint the background of the image (Boolean)") |
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559 (OPTION_COLOR, boost::program_options::value<std::string>(), |
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560 "Color of the background (e.g. \"255,0,0\")") |
0 | 561 ; |
562 | |
563 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
564 pyramid.add_options() | |
129
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565 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
0 | 566 "Reconstruct the full pyramid (slow) (Boolean)") |
129
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567 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
0 | 568 "Apply smoothing when reconstructing the pyramid " |
569 "(slower, but higher quality) (Boolean)") | |
129
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570 (OPTION_LEVELS, boost::program_options::value<int>(), |
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571 "Number of levels in the target pyramid") |
0 | 572 ; |
573 | |
574 boost::program_options::options_description target("Options for the target image"); | |
575 target.add_options() | |
129
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576 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
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577 "Width of the tiles in the target image") |
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578 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
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579 "Height of the tiles in the target image") |
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580 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
0 | 581 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
129
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582 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
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583 "Set quality level for JPEG (0..100)") |
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584 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
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585 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
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586 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
0 | 587 "Folder where to store the output DICOM instances") |
129
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588 (OPTION_FOLDER_PATTERN, |
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589 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
0 | 590 "Pattern for the files in the output folder") |
591 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
592 "URL to the REST API of the target Orthanc server") | |
593 ; | |
594 | |
595 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
596 volumeOptions.add_options() | |
129
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597 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>()->default_value(15), |
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598 "Width of the specimen (in mm)") |
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599 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>()->default_value(15), |
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600 "Height of the specimen (in mm)") |
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601 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
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602 "Depth of the specimen (in mm)") |
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603 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
0 | 604 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
129
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605 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
0 | 606 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
607 ; | |
608 | |
129
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609 boost::program_options::options_description restOptions |
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610 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
125
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611 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
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612 |
0 | 613 boost::program_options::options_description advancedOptions("Advanced options"); |
614 advancedOptions.add_options() | |
129
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615 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
0 | 616 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
129
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617 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
0 | 618 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
129
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619 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
0 | 620 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
129
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621 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
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622 "Number of pyramid levels up to which multithreading " |
0 | 623 "should be applied (only for performance/memory tuning)") |
624 ; | |
625 | |
626 boost::program_options::options_description hidden; | |
627 hidden.add_options() | |
129
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628 (OPTION_INPUT, boost::program_options::value<std::string>(), |
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629 "Input file"); |
0 | 630 ; |
631 | |
632 boost::program_options::options_description allWithoutHidden; | |
125
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633 allWithoutHidden |
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634 .add(generic) |
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635 .add(source) |
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636 .add(pyramid) |
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637 .add(target) |
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638 .add(volumeOptions) |
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639 .add(restOptions) |
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640 .add(advancedOptions); |
0 | 641 |
642 boost::program_options::options_description all = allWithoutHidden; | |
643 all.add(hidden); | |
644 | |
645 boost::program_options::positional_options_description positional; | |
129
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646 positional.add(OPTION_INPUT, 1); |
0 | 647 |
648 boost::program_options::variables_map options; | |
649 bool error = false; | |
650 | |
651 try | |
652 { | |
653 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
654 options(all).positional(positional).run(), options); | |
655 boost::program_options::notify(options); | |
656 } | |
657 catch (boost::program_options::error& e) | |
658 { | |
659 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
660 error = true; | |
661 } | |
662 | |
663 if (!error && | |
129
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664 options.count(OPTION_SAMPLE_DATASET)) |
0 | 665 { |
666 std::string sample; | |
667 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
668 | |
669 std::cout << std::endl << sample << std::endl; | |
670 | |
671 return false; | |
672 } | |
673 | |
674 if (!error && | |
129
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675 options.count(OPTION_HELP) == 0 && |
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676 options.count(OPTION_VERSION) == 0 && |
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677 options.count(OPTION_INPUT) != 1) |
0 | 678 { |
679 LOG(ERROR) << "No input file was specified"; | |
680 error = true; | |
681 } | |
682 | |
129
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683 if (error || options.count(OPTION_HELP)) |
0 | 684 { |
685 std::cout << std::endl | |
686 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
687 << std::endl | |
688 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
689 << std::endl << std::endl | |
690 << "Create a DICOM file from a digital pathology image." | |
691 << std::endl; | |
692 | |
693 std::cout << allWithoutHidden << "\n"; | |
694 | |
695 if (error) | |
696 { | |
697 exitStatus = -1; | |
698 } | |
699 | |
700 return false; | |
701 } | |
702 | |
129
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703 if (options.count(OPTION_VERSION)) |
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704 { |
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705 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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706 return false; |
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707 } |
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708 |
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709 if (options.count(OPTION_VERBOSE)) |
0 | 710 { |
711 Orthanc::Logging::EnableInfoLevel(true); | |
712 } | |
713 | |
129
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714 if (options.count(OPTION_OPENSLIDE)) |
0 | 715 { |
129
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716 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
0 | 717 } |
718 | |
129
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719 if (options.count(OPTION_PYRAMID) && |
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720 options[OPTION_PYRAMID].as<bool>()) |
0 | 721 { |
722 parameters.SetReconstructPyramid(true); | |
723 } | |
724 | |
129
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725 if (options.count(OPTION_SMOOTH) && |
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726 options[OPTION_SMOOTH].as<bool>()) |
0 | 727 { |
728 parameters.SetSmoothEnabled(true); | |
729 } | |
730 | |
129
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731 if (options.count(OPTION_SAFETY) && |
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732 options[OPTION_SAFETY].as<bool>()) |
0 | 733 { |
734 parameters.SetSafetyCheck(true); | |
735 } | |
736 | |
129
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737 if (options.count(OPTION_REENCODE) && |
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738 options[OPTION_REENCODE].as<bool>()) |
0 | 739 { |
740 parameters.SetForceReencode(true); | |
741 } | |
742 | |
129
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743 if (options.count(OPTION_REPAINT) && |
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744 options[OPTION_REPAINT].as<bool>()) |
0 | 745 { |
746 parameters.SetRepaintBackground(true); | |
747 } | |
748 | |
129
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749 if (options.count(OPTION_TILE_WIDTH) || |
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750 options.count(OPTION_TILE_HEIGHT)) |
0 | 751 { |
752 int w = 0; | |
129
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753 if (options.count(OPTION_TILE_WIDTH)) |
0 | 754 { |
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755 w = options[OPTION_TILE_WIDTH].as<int>(); |
0 | 756 } |
757 | |
145 | 758 int h = 0; |
129
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759 if (options.count(OPTION_TILE_HEIGHT)) |
0 | 760 { |
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761 h = options[OPTION_TILE_HEIGHT].as<int>(); |
0 | 762 } |
763 | |
764 if (w < 0 || h < 0) | |
765 { | |
766 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
767 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
768 } | |
769 | |
770 parameters.SetTargetTileSize(w, h); | |
771 } | |
772 | |
129
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773 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
0 | 774 |
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775 if (options.count(OPTION_COLOR)) |
0 | 776 { |
777 uint8_t r, g, b; | |
129
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778 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
0 | 779 parameters.SetBackgroundColor(r, g, b); |
780 } | |
781 | |
129
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782 if (options.count(OPTION_COMPRESSION)) |
0 | 783 { |
129
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784 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
0 | 785 if (s == "none") |
786 { | |
787 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
788 } | |
789 else if (s == "jpeg") | |
790 { | |
791 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
792 } | |
793 else if (s == "jpeg2000") | |
794 { | |
795 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
796 } | |
797 else | |
798 { | |
799 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
800 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
801 } | |
802 } | |
803 | |
129
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804 if (options.count(OPTION_JPEG_QUALITY)) |
0 | 805 { |
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806 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
0 | 807 } |
808 | |
129
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809 if (options.count(OPTION_LEVELS)) |
0 | 810 { |
129
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811 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
0 | 812 } |
813 | |
129
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814 if (options.count(OPTION_LOWER_LEVELS)) |
0 | 815 { |
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816 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
0 | 817 } |
818 | |
129
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819 if (options.count(OPTION_THREADS)) |
0 | 820 { |
129
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821 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
0 | 822 } |
823 | |
129
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824 if (options.count(OPTION_MAX_SIZE)) |
0 | 825 { |
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826 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
0 | 827 } |
828 | |
129
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829 if (options.count(OPTION_FOLDER)) |
0 | 830 { |
129
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831 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
0 | 832 } |
833 | |
129
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834 if (options.count(OPTION_FOLDER_PATTERN)) |
0 | 835 { |
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836 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
0 | 837 } |
838 | |
125
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839 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
0 | 840 |
129
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841 if (options.count(OPTION_DATASET)) |
0 | 842 { |
129
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843 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
0 | 844 } |
845 | |
129
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846 if (options.count(OPTION_IMAGED_WIDTH)) |
0 | 847 { |
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848 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
0 | 849 } |
850 | |
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851 if (options.count(OPTION_IMAGED_HEIGHT)) |
0 | 852 { |
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853 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
0 | 854 } |
855 | |
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856 if (options.count(OPTION_IMAGED_DEPTH)) |
0 | 857 { |
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858 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
0 | 859 } |
860 | |
129
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861 if (options.count(OPTION_OFFSET_X)) |
0 | 862 { |
129
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863 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
0 | 864 } |
865 | |
129
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866 if (options.count(OPTION_OFFSET_Y)) |
0 | 867 { |
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868 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
0 | 869 } |
870 | |
129
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871 if (options.count(OPTION_OPTICAL_PATH)) |
0 | 872 { |
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873 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
0 | 874 if (s == "none") |
875 { | |
876 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
877 } | |
878 else if (s == "brightfield") | |
879 { | |
880 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
881 } | |
882 else | |
883 { | |
884 LOG(ERROR) << "Unknown optical path definition: " << s; | |
885 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
886 } | |
887 } | |
888 | |
129
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889 if (options.count(OPTION_ICC_PROFILE)) |
0 | 890 { |
129
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891 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
0 | 892 } |
893 | |
894 return true; | |
895 } | |
896 | |
897 | |
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898 |
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899 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
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900 const std::string& path, |
0 | 901 const OrthancWSI::DicomizerParameters& parameters) |
902 { | |
903 LOG(WARNING) << "The input image is: " << path; | |
904 | |
905 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
906 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
907 | |
908 switch (format) | |
909 { | |
910 case OrthancWSI::ImageCompression_Png: | |
57
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911 { |
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912 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 913 return new OrthancWSI::TiledPngImage(path, |
914 parameters.GetTargetTileWidth(512), | |
915 parameters.GetTargetTileHeight(512)); | |
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916 } |
0 | 917 |
918 case OrthancWSI::ImageCompression_Jpeg: | |
57
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919 { |
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920 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 921 return new OrthancWSI::TiledJpegImage(path, |
922 parameters.GetTargetTileWidth(512), | |
923 parameters.GetTargetTileHeight(512)); | |
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924 } |
0 | 925 |
926 case OrthancWSI::ImageCompression_Tiff: | |
927 { | |
928 try | |
929 { | |
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930 std::unique_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
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931 sourceCompression = tiff->GetImageCompression(); |
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932 return tiff.release(); |
0 | 933 } |
934 catch (Orthanc::OrthancException&) | |
935 { | |
936 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
937 } | |
938 } | |
939 | |
940 default: | |
941 break; | |
942 } | |
943 | |
944 try | |
945 { | |
946 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
57
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947 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 948 return new OrthancWSI::OpenSlidePyramid(path, |
949 parameters.GetTargetTileWidth(512), | |
950 parameters.GetTargetTileHeight(512)); | |
951 } | |
952 catch (Orthanc::OrthancException&) | |
953 { | |
954 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
955 return NULL; | |
956 } | |
957 } | |
958 | |
959 | |
960 int main(int argc, char* argv[]) | |
961 { | |
962 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
93
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963 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
0 | 964 |
965 int exitStatus = 0; | |
966 | |
967 try | |
968 { | |
969 OrthancWSI::DicomizerParameters parameters; | |
970 OrthancWSI::ImagedVolumeParameters volume; | |
971 | |
972 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
973 { | |
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974 OrthancWSI::ImageCompression sourceCompression; |
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975 std::unique_ptr<OrthancWSI::ITiledPyramid> source; |
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976 |
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977 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters)); |
0 | 978 if (source.get() == NULL) |
979 { | |
980 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
981 } | |
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982 |
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983 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
0 | 984 |
985 // Create the shared DICOM tags | |
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986 std::unique_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); |
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987 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
0 | 988 |
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989 std::unique_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); |
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990 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
0 | 991 } |
992 } | |
993 catch (Orthanc::OrthancException& e) | |
994 { | |
995 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
996 exitStatus = -1; | |
997 } | |
998 | |
999 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
1000 | |
1001 return exitStatus; | |
1002 } |